Itunes reorganized and erased my original music files ;(

I keep all of my music on an external hard drive (Western Digital passport 320) and had it organized very specifically. I recently imported it all into itunes to put onto my ipod and checked "keep itunes music folder organized" with the location on my external drive. I thought this meant there would be a copy organized in itunes style. But what ended up happening was my music is now completely unrecognizable; there are a million more folders and songs are not in their proper place. There is NO way I can reorganize this because many of the mp3s were organized by folder and the names of the songs were track 1 etc.
Is there anything I can do to restore my previous organization?

Thanks Chris. Another question for you. I cannot authorize my computer now. The error message says that there was an error storing your authorization information on this computer. The required directory was not found or has a permission error. Correct this permission problem and try again, or deauthorizse this computer if the permissions cannot be changed.
Well I deauthorized all in the settings in iTunes, not it won't let me authorize it now,
Any suggestions?
Thanks

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